File Changes for angie

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• src/hg/hgTables/hgTables.c
  • lines changed 48, context: html, text, full: html, text
    Feature #3707 (VCF in hgTables): Brooke pointed out the annoyance ofVCF custom track's hyperlinks output setting vis to full when it was already pack. Turns out that the canPack info for all custom tracks was being discarded due to use of hTrackOpenVis which looks for trackDb in database. We usually already have the tdb anyway, so when it's available, look at tdb->canPack and set vis only if the track is currently hidden. Also, while looking into a timeout case that Brooke identified, I noticed that hgTables wasn't calling knetUdc so it was using samtools & tabix's knetfile library instead of our own -- fixed.
• src/hg/hgTables/vcf.c
  • lines changed 3, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
  • lines changed 14, context: html, text, full: html, text
    Feature #3707 (VCF in hgTables): when calling vcf.c's addFilteredBedsOnRegion ina loop, apply maxOut cumulatively, instead of separately for each region. Unfortunately, some higher-level code calls vcfGetFilteredBedsOnRegions with one region at a time, so it doesn't know it's running in a loop. The check for maxOut needs to move up to top-level (e.g. doSummaryStats), or VCF needs its own top-level routines, or a true genome-wide query needs to be possible in hgTables.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 7, context: html, text, full: html, text
    Feature #3711 (VCF haplotype-sorting display): Fixed a silly boundary& rounding error in pixel loop. Also, use lower case for alternate allele in cluster mouseovers so the relationship to blue and red pixels is more clear.
  • lines changed 1, context: html, text, full: html, text
    Fix for buffer overflow case found by Brooke, in vcfToPgSnp allele-abbreviating code.
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
  • lines changed 164, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults: 1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black. Draw top & bottom bounds of variants in extra pixel rows. 2. Draw the tree using open triangles instead of open rectangles.
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    oops, forgot cartSaveSession() in VCF details page's little form to anchor haplotype sorting to this variant.
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 2, context: html, text, full: html, text
    Feature #2822 (VCF customFactory): Fixing typo caught by Brooke.
• src/hg/inc/vcfUi.h
  • lines changed 7, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults: 1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black. Draw top & bottom bounds of variants in extra pixel rows. 2. Draw the tree using open triangles instead of open rectangles.
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    Feature #3711 (VCF haplotype-sorting display): reduce min height to 4, because there can be as few as 4 haplotypes to sort.
  • lines changed 16, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added section headers forhaplo-sorting display and filters; added some explanatory text at the beginning of the haplo-sorting section.
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
  • lines changed 26, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults: 1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black. Draw top & bottom bounds of variants in extra pixel rows. 2. Draw the tree using open triangles instead of open rectangles.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Tweak to make less editing work in the future: derive dated directoryname from output of date command instead of search & replace.
• src/inc/vcf.h
  • lines changed 6, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.
• src/lib/tests/vcfParseTest.c
  • lines changed 1, context: html, text, full: html, text
    Oops, forgot to run 'make test' before committing, and overlookeda test program...
• src/lib/vcf.c
  • lines changed 25, context: html, text, full: html, text
    MLQ #6136: adding support for VCF 3.3 header line formats.
  • lines changed 9, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number of records to retrieve in vcfTabixFileMayOpen.